Starting phenix.real_space_refine on Mon Sep 23 13:09:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7n_24299/09_2024/7r7n_24299.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7n_24299/09_2024/7r7n_24299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7n_24299/09_2024/7r7n_24299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7n_24299/09_2024/7r7n_24299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7n_24299/09_2024/7r7n_24299.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7n_24299/09_2024/7r7n_24299.cif" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 1795 2.51 5 N 481 2.21 5 O 497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2790 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 735 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 3 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1382 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 61 Chain: "L" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 635 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 87} Chain breaks: 2 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 2.99, per 1000 atoms: 1.07 Number of scatterers: 2790 At special positions: 0 Unit cell: (77.7, 66.15, 76.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 497 8.00 N 481 7.00 C 1795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.12 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.09 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.21 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " BETA1-6 " NAG A 1 " - " FUC A 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN E 343 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 327.2 milliseconds 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 714 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 12.3% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.413A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.667A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.667A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.537A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.320A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.603A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.564A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.564A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 297 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.79 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 808 1.33 - 1.46: 747 1.46 - 1.58: 1283 1.58 - 1.71: 0 1.71 - 1.83: 20 Bond restraints: 2858 Sorted by residual: bond pdb=" NE ARG L 18 " pdb=" CZ ARG L 18 " ideal model delta sigma weight residual 1.326 1.367 -0.041 1.10e-02 8.26e+03 1.40e+01 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.470 -0.057 2.00e-02 2.50e+03 8.07e+00 bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.582 -0.052 2.00e-02 2.50e+03 6.86e+00 bond pdb=" CB LEU E 517 " pdb=" CG LEU E 517 " ideal model delta sigma weight residual 1.530 1.579 -0.049 2.00e-02 2.50e+03 5.94e+00 bond pdb=" C5 FUC A 3 " pdb=" O5 FUC A 3 " ideal model delta sigma weight residual 1.423 1.471 -0.048 2.00e-02 2.50e+03 5.81e+00 ... (remaining 2853 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 3270 1.51 - 3.02: 527 3.02 - 4.53: 68 4.53 - 6.04: 28 6.04 - 7.54: 14 Bond angle restraints: 3907 Sorted by residual: angle pdb=" C GLY H 27 " pdb=" N PRO H 28 " pdb=" CA PRO H 28 " ideal model delta sigma weight residual 119.85 127.39 -7.54 1.01e+00 9.80e-01 5.58e+01 angle pdb=" C SER E 383 " pdb=" N PRO E 384 " pdb=" CA PRO E 384 " ideal model delta sigma weight residual 119.56 126.71 -7.15 1.02e+00 9.61e-01 4.91e+01 angle pdb=" C GLN E 498 " pdb=" N PRO E 499 " pdb=" CA PRO E 499 " ideal model delta sigma weight residual 119.87 126.95 -7.08 1.04e+00 9.25e-01 4.63e+01 angle pdb=" C ALA L 43 " pdb=" N PRO L 44 " pdb=" CA PRO L 44 " ideal model delta sigma weight residual 119.85 126.57 -6.72 1.01e+00 9.80e-01 4.42e+01 angle pdb=" C PHE E 490 " pdb=" N PRO E 491 " pdb=" CA PRO E 491 " ideal model delta sigma weight residual 119.87 126.77 -6.90 1.04e+00 9.25e-01 4.40e+01 ... (remaining 3902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.05: 1577 13.05 - 26.10: 77 26.10 - 39.14: 14 39.14 - 52.19: 9 52.19 - 65.24: 6 Dihedral angle restraints: 1683 sinusoidal: 561 harmonic: 1122 Sorted by residual: dihedral pdb=" CB CYS H 103 " pdb=" SG CYS H 103 " pdb=" SG CYS H 108 " pdb=" CB CYS H 108 " ideal model delta sinusoidal sigma weight residual -86.00 -151.24 65.24 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 45.49 47.51 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 62.52 30.48 1 1.00e+01 1.00e-02 1.33e+01 ... (remaining 1680 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.057: 306 0.057 - 0.114: 93 0.114 - 0.171: 26 0.171 - 0.228: 9 0.228 - 0.285: 6 Chirality restraints: 440 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.12e+01 chirality pdb=" C1 FUC A 3 " pdb=" O6 NAG A 1 " pdb=" C2 FUC A 3 " pdb=" O5 FUC A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.68e+00 chirality pdb=" C2 NAG A 2 " pdb=" C1 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" N2 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.78 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 437 not shown) Planarity restraints: 505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 489 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C TYR E 489 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR E 489 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE E 490 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 92 " -0.021 2.00e-02 2.50e+03 1.12e-02 2.53e+00 pdb=" CG TYR L 92 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR L 92 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR L 92 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR L 92 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR L 92 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR L 92 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 92 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 449 " 0.019 2.00e-02 2.50e+03 1.06e-02 2.23e+00 pdb=" CG TYR E 449 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR E 449 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR E 449 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR E 449 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR E 449 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 449 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 449 " 0.017 2.00e-02 2.50e+03 ... (remaining 502 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 1515 3.02 - 3.49: 2477 3.49 - 3.96: 4310 3.96 - 4.43: 4896 4.43 - 4.90: 7917 Nonbonded interactions: 21115 Sorted by model distance: nonbonded pdb=" N ASP E 428 " pdb=" OD1 ASP E 428 " model vdw 2.553 3.120 nonbonded pdb=" N LYS E 462 " pdb=" O LYS E 462 " model vdw 2.609 2.496 nonbonded pdb=" N GLN L 3 " pdb=" OE1 GLN L 3 " model vdw 2.616 3.120 nonbonded pdb=" N THR H 76 " pdb=" N SER H 77 " model vdw 2.623 2.560 nonbonded pdb=" N ALA E 372 " pdb=" N SER E 373 " model vdw 2.627 2.560 ... (remaining 21110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.320 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.057 2858 Z= 0.670 Angle : 1.245 7.544 3907 Z= 0.835 Chirality : 0.069 0.285 440 Planarity : 0.005 0.016 504 Dihedral : 9.309 63.153 948 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.45 % Allowed : 0.90 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.43), residues: 373 helix: -4.27 (0.43), residues: 26 sheet: 0.66 (0.46), residues: 126 loop : 0.27 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.005 TRP L 35 PHE 0.016 0.003 PHE L 98 TYR 0.021 0.004 TYR L 92 ARG 0.003 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8454 (mp10) cc_final: 0.8035 (tp40) REVERT: E 513 LEU cc_start: 0.8949 (mt) cc_final: 0.8631 (tt) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.1850 time to fit residues: 21.2206 Evaluate side-chains 56 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 2858 Z= 0.341 Angle : 0.685 9.904 3907 Z= 0.358 Chirality : 0.049 0.204 440 Planarity : 0.004 0.027 504 Dihedral : 5.340 50.530 484 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 6.73 % Allowed : 15.70 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.42), residues: 373 helix: -3.64 (0.86), residues: 20 sheet: 0.70 (0.46), residues: 130 loop : 0.04 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 PHE 0.019 0.002 PHE H 29 TYR 0.018 0.002 TYR H 95 ARG 0.005 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 59 time to evaluate : 0.318 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8285 (mp10) cc_final: 0.7930 (tp40) REVERT: E 349 SER cc_start: 0.8351 (OUTLIER) cc_final: 0.8065 (t) REVERT: E 513 LEU cc_start: 0.9091 (mt) cc_final: 0.8709 (tt) REVERT: L 49 TYR cc_start: 0.8159 (p90) cc_final: 0.7831 (p90) REVERT: L 96 ARG cc_start: 0.7257 (ttt-90) cc_final: 0.6783 (ttm170) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 0.1262 time to fit residues: 10.3213 Evaluate side-chains 62 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 51 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 0.0670 chunk 27 optimal weight: 0.0970 chunk 22 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.0980 chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.1980 overall best weight: 0.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2858 Z= 0.169 Angle : 0.578 5.991 3907 Z= 0.298 Chirality : 0.045 0.138 440 Planarity : 0.004 0.027 504 Dihedral : 4.833 44.481 484 Min Nonbonded Distance : 2.643 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 6.73 % Allowed : 17.49 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.43), residues: 373 helix: -3.16 (0.91), residues: 26 sheet: 0.93 (0.47), residues: 119 loop : 0.01 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 PHE 0.033 0.002 PHE E 374 TYR 0.013 0.001 TYR E 423 ARG 0.004 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 62 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8217 (mp10) cc_final: 0.7903 (tp40) REVERT: E 349 SER cc_start: 0.8132 (OUTLIER) cc_final: 0.7921 (t) REVERT: E 513 LEU cc_start: 0.9034 (mt) cc_final: 0.8579 (tt) REVERT: L 49 TYR cc_start: 0.8124 (p90) cc_final: 0.7549 (p90) outliers start: 15 outliers final: 10 residues processed: 70 average time/residue: 0.1135 time to fit residues: 10.0005 Evaluate side-chains 65 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 54 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.1980 chunk 22 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 9 optimal weight: 0.1980 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 2858 Z= 0.295 Angle : 0.628 7.594 3907 Z= 0.322 Chirality : 0.046 0.151 440 Planarity : 0.005 0.057 504 Dihedral : 5.299 40.299 484 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 6.28 % Allowed : 18.39 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.42), residues: 373 helix: -2.71 (1.07), residues: 26 sheet: 0.85 (0.47), residues: 119 loop : -0.29 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 PHE 0.024 0.002 PHE H 29 TYR 0.014 0.001 TYR H 95 ARG 0.008 0.001 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.328 Fit side-chains REVERT: H 3 GLN cc_start: 0.8297 (mp10) cc_final: 0.7995 (tp40) REVERT: E 442 ASP cc_start: 0.8853 (t0) cc_final: 0.8629 (t0) REVERT: E 513 LEU cc_start: 0.9098 (mt) cc_final: 0.8653 (tt) REVERT: L 49 TYR cc_start: 0.8205 (p90) cc_final: 0.7738 (p90) outliers start: 14 outliers final: 13 residues processed: 61 average time/residue: 0.1112 time to fit residues: 8.6959 Evaluate side-chains 62 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 24 optimal weight: 0.0020 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 chunk 7 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 2858 Z= 0.245 Angle : 0.592 6.355 3907 Z= 0.305 Chirality : 0.045 0.137 440 Planarity : 0.004 0.031 504 Dihedral : 5.045 37.575 484 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 6.28 % Allowed : 18.83 % Favored : 74.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.43), residues: 373 helix: -2.59 (1.08), residues: 26 sheet: 0.98 (0.48), residues: 118 loop : -0.44 (0.40), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 PHE 0.019 0.002 PHE H 29 TYR 0.013 0.001 TYR L 92 ARG 0.002 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.313 Fit side-chains REVERT: H 3 GLN cc_start: 0.8224 (mp10) cc_final: 0.7979 (tp40) REVERT: E 513 LEU cc_start: 0.9089 (mt) cc_final: 0.8629 (tt) REVERT: L 2 ILE cc_start: 0.7572 (mt) cc_final: 0.7294 (pt) REVERT: L 49 TYR cc_start: 0.8227 (p90) cc_final: 0.7815 (p90) outliers start: 14 outliers final: 14 residues processed: 63 average time/residue: 0.1251 time to fit residues: 10.0959 Evaluate side-chains 66 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 52 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 2858 Z= 0.428 Angle : 0.701 6.891 3907 Z= 0.368 Chirality : 0.047 0.153 440 Planarity : 0.005 0.029 504 Dihedral : 5.788 29.248 482 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 8.97 % Allowed : 18.83 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.43), residues: 373 helix: -2.41 (1.08), residues: 26 sheet: 0.92 (0.50), residues: 114 loop : -0.70 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 PHE 0.015 0.002 PHE E 486 TYR 0.014 0.002 TYR H 95 ARG 0.008 0.001 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 55 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8385 (mp10) cc_final: 0.8007 (tp40) REVERT: E 513 LEU cc_start: 0.9117 (mt) cc_final: 0.8690 (tt) REVERT: L 49 TYR cc_start: 0.8341 (p90) cc_final: 0.7952 (p90) outliers start: 20 outliers final: 16 residues processed: 66 average time/residue: 0.1092 time to fit residues: 9.2111 Evaluate side-chains 69 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 53 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 10 optimal weight: 0.0970 chunk 7 optimal weight: 0.0770 chunk 6 optimal weight: 0.6980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 34 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.4851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 2858 Z= 0.201 Angle : 0.608 6.234 3907 Z= 0.312 Chirality : 0.045 0.128 440 Planarity : 0.004 0.025 504 Dihedral : 4.920 26.622 482 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 4.93 % Allowed : 21.97 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.43), residues: 373 helix: -2.33 (0.95), residues: 33 sheet: 0.89 (0.49), residues: 112 loop : -0.70 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 PHE 0.014 0.002 PHE E 392 TYR 0.011 0.001 TYR E 473 ARG 0.002 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8266 (mp10) cc_final: 0.7981 (tp40) REVERT: H 29 PHE cc_start: 0.8144 (t80) cc_final: 0.7699 (t80) REVERT: E 467 ASP cc_start: 0.7539 (t0) cc_final: 0.7045 (p0) REVERT: E 513 LEU cc_start: 0.9107 (mt) cc_final: 0.8642 (tt) REVERT: L 49 TYR cc_start: 0.8182 (p90) cc_final: 0.7803 (p90) outliers start: 11 outliers final: 11 residues processed: 64 average time/residue: 0.1177 time to fit residues: 9.5136 Evaluate side-chains 63 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 52 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 2858 Z= 0.445 Angle : 0.710 6.290 3907 Z= 0.371 Chirality : 0.048 0.163 440 Planarity : 0.005 0.030 504 Dihedral : 5.936 35.596 482 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 5.38 % Allowed : 22.42 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.42), residues: 373 helix: -2.42 (1.02), residues: 26 sheet: 0.74 (0.48), residues: 114 loop : -1.02 (0.38), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 PHE 0.016 0.002 PHE E 486 TYR 0.012 0.002 TYR H 95 ARG 0.006 0.001 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8373 (mp10) cc_final: 0.8040 (tp40) REVERT: E 513 LEU cc_start: 0.9136 (mt) cc_final: 0.8690 (tt) REVERT: L 49 TYR cc_start: 0.8306 (p90) cc_final: 0.8015 (p90) outliers start: 12 outliers final: 12 residues processed: 60 average time/residue: 0.1140 time to fit residues: 8.7248 Evaluate side-chains 65 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 53 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.0980 chunk 10 optimal weight: 0.0870 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.0070 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 16 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 overall best weight: 0.1776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.5232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 2858 Z= 0.195 Angle : 0.628 6.381 3907 Z= 0.322 Chirality : 0.045 0.133 440 Planarity : 0.005 0.035 504 Dihedral : 4.927 31.263 482 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 5.83 % Allowed : 24.66 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.43), residues: 373 helix: -3.29 (0.80), residues: 33 sheet: 0.75 (0.47), residues: 114 loop : -0.80 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 PHE 0.019 0.002 PHE H 29 TYR 0.011 0.001 TYR E 473 ARG 0.004 0.001 ARG E 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8204 (mp10) cc_final: 0.7977 (tp40) REVERT: H 29 PHE cc_start: 0.8095 (t80) cc_final: 0.7650 (t80) REVERT: E 386 LYS cc_start: 0.9308 (mmtm) cc_final: 0.7545 (pttt) REVERT: E 513 LEU cc_start: 0.9121 (mt) cc_final: 0.8634 (tt) REVERT: L 49 TYR cc_start: 0.8177 (p90) cc_final: 0.7857 (p90) outliers start: 13 outliers final: 13 residues processed: 65 average time/residue: 0.1345 time to fit residues: 10.7497 Evaluate side-chains 70 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 57 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 468 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 17 optimal weight: 0.0570 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 overall best weight: 0.3696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 2858 Z= 0.256 Angle : 0.630 6.421 3907 Z= 0.321 Chirality : 0.045 0.129 440 Planarity : 0.005 0.029 504 Dihedral : 5.093 34.362 482 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 5.38 % Allowed : 24.66 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.43), residues: 373 helix: -3.37 (0.78), residues: 33 sheet: 0.76 (0.47), residues: 114 loop : -0.86 (0.40), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 PHE 0.011 0.002 PHE E 392 TYR 0.010 0.001 TYR E 473 ARG 0.007 0.001 ARG L 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8259 (mp10) cc_final: 0.8020 (tp40) REVERT: H 29 PHE cc_start: 0.8056 (t80) cc_final: 0.7590 (t80) REVERT: E 513 LEU cc_start: 0.9134 (mt) cc_final: 0.8633 (tt) REVERT: L 49 TYR cc_start: 0.8159 (p90) cc_final: 0.7869 (p90) outliers start: 12 outliers final: 12 residues processed: 61 average time/residue: 0.1172 time to fit residues: 8.9795 Evaluate side-chains 66 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 54 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 14 optimal weight: 0.0570 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.091411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.083830 restraints weight = 7385.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.085570 restraints weight = 4187.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086781 restraints weight = 2669.827| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 2858 Z= 0.360 Angle : 0.693 7.835 3907 Z= 0.357 Chirality : 0.046 0.131 440 Planarity : 0.005 0.034 504 Dihedral : 5.704 40.279 482 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.28 % Allowed : 24.66 % Favored : 69.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.42), residues: 373 helix: -3.47 (0.75), residues: 33 sheet: 0.65 (0.47), residues: 114 loop : -1.10 (0.39), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 PHE 0.013 0.002 PHE E 374 TYR 0.011 0.001 TYR E 423 ARG 0.008 0.001 ARG L 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1201.99 seconds wall clock time: 21 minutes 42.67 seconds (1302.67 seconds total)